matchFeatures implements a generic feature matching algorithm. Feature matching for stereo is a much more constrained problem, where you are only matching features in one image to features in the vicinity of that feature in the other image.
This spatial constraint makes it a very different problem.
If your end goal is to find the depth map, look at this example below:
Another suggestion is to use the epipolar constraint with RANSAC to eliminate outliers in the feature matching as shown in step 4 below:
